Materials and methods Cell culture and transfection. The human osteosarcoma cell line U2OS, human cervical cancer cell line HeLa, mouse embryo fibroblast cell line NIH3T3, and human embryonic kidney HEK293T cell line were obtained from ATCC. The cells were cultured in DMEM (ThermoFisher Scientific) supplemented with 10% FBS and NEAA according to the provided protocol. For serum starvation, cells were cultured with DMEM without serum for several time points. For amino acids starvation, cells were cultured with medium without amino acids for 48h. For high salt treatment, cells were cultured with 190mM NaCl for 48h. For 1,6-hexanediol treatment, cells were treated with 10% 1,6-hexanediol for 2min at room temperature. Plasmids were transfected into cells using polyethyleneimine (PEI) according to the operation instructions. Plasmid construction. ORFs were amplified by PCR from cDNA (derived from AML12 cells cells). The PCR products were digested with BamHI (AscI) and MluI and cloned into the retroviral vector Lv-EF1a-GFP-MCS-IRES-puro. For RNAi experiments, shRNA plasmids were constructed by cloning the target sequences to the pLKO.1-puro vector: GAAATTCCAGACAATGTT AGA (shKDM7A-1), GTATAACTTCCACATTACAGT (shKDM7A-2) and ACTCGACAC TATAGTATCTCA (shControl). FRAP. The FRAP assay was performed in a live-cell chamber with confocal laser scanning microscopy. The bleaching duration was about 4 s in an area of one nuclear body. Images were captured at 1.3-s interval for 40 time points. The data were processed with LAS AF Lite. Live-cell imaging. Live-cell imaging experiments were performed on a GE DeltaVision inverted microscope. Images of U2OS cells were captured every 10 min for a total of 10 h. The data were processed with the Volocity software. Western blotting. Cells lysates were separated by SDS-PAGE and then transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore). After washing and blocking, the membranes were incubated with primary antibodies as follows: anti-β-actin (66009-1-Ig, Proteintech), anti-GAPDH (9600, AGOMA), anti-H3 (AF0009, Beyotime), anti-MCM7 (sc-9966, Santa Cruz) and anti-KDM7A (raised against amino acids 417-735 in rabbit, ABclonal). The blots were detected with HRP-coupled secondary antibodies. Immunofluorescence. Immunofluorescence was performed as described elsewhere (Zhang et al., 2015). Besides those used for western blotting, other primary antibodies were: anti-SC35 (ab11826, Abcam), anti-PML (A1184, ABclonal; 05-718, Merck Millipore), anti-PSPC1 (SC-374387, Santa Cruz), anti-COIL (SC-55594, Santa Cruz), anti-Sam68 (sc-1238, Santa Cruz), anti-BMI1 (sc-390443, Santa Cruz) anti-C23 (10556-1-AP, Proteintech), anti-H3 (ab1791, Abcam) and MCM7 (sc-9966, Santa Cruz). The slides were assessed with a confocal laser scanning microscopy (Leica, SP5 and SP8). Cell cycle assay. The samples were prepared with the cell cycle and apoptosis analysis kit (Beyotime), and then analyzed using a FACSCalibur flow cytometer (BD). TEM with HRP-DAB. The NIH3T3 cells and mouse testis (Department of Laboratory Animal Science provided guidance on the study protocol) were fixed with 4% formaldehyde and incubated with the KDM7A antibody. The primary antibody was detected using an HRP secondary antibody. Then, DAB (P0203, Beyotime) was used for the HRP staining, which is EM-visible. After that, the samples were prepared for conventional TEM. The sections were stained and imaged at the EM facility of ION (Institute of Neuroscience, Shanghai, China). Immunoprecipitation and mass spectrometry. The U2OS cells were transfected with GFP-only or GFP-KDM7A plasmids for 24 h and then harvested. The nuclear extracts were prepared from 20 million cells and were incubated with 20  L GFP-TRAP_M (gtm-20, Chromotek) in 50 mM Tris HCl (pH 7.5), 125 mM NaCl,

0.2% NP-40, 5% glycerol, 1.5 mM MgCl2, and protease inhibitors. The LC-MS/MS experiments and data analysis were performed as described elsewhere (Zhang et al., 2015). The experiments were conducted using three biological replicates, and the appeared three times in the GFP-KDM7A group but not more than once in the GFP-only group were considered as candidates. For IP/MS assay in HeLa cells under 0% FBS, cells were harvested after cultured in 0% FBS for 48h, with IgG as control. The proteins appeared more than two times in KDM7A group but not more than once in control group were considered as candidates. purification. The KDM7A and C-terminal of KDM7A cDNA was cloned into the pCAG-6xHis-GFP -KDM7A plasmid and then transfected into HEK293T cells. The proteins were purified with Ni Aogarose 6 FF (AOGMA) with the AKTA system (GE Healthcare Life Sciences). The proteins were then concentrated in an Amicon Ultracel-50K spin concentrator and was exchanged to storage buffer [50 mM Tris-HCl( pH 7.5), 200 mM NaCl, 1 mM DTT, 10% glycerol]. The concentrated proteins were stored in -80°C freezer after flash freezing in liquid nitrogen. Liquid droplet assay. For the droplet assay, proteins were dropped on the living cell chamber at concentrations of 0.25, 0.5, 1, 2, 3 μM in the reaction buffer [50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM DTT], and then imaged with a confocal laser scanning microscopy (Leica, SP5). For DNA contained droplet assays, genomic DNA was extracted from NIH3T3 cells and was sheered by sonication to lengths within the range of 300-700 bp. DNA was added to the protein solution at different concentrations and then imaged with a confocal laser scanning microscope (Leica, SP5). Supplementary figure legends Fig. S1: KDM7A marks a type of (K-bodies) in serum starved Hela cells. (A) The separated images of co-staining of KDM7A and SC35, PSPC1, PML, Coilin, BMI1 and Sam68 in Hela cells treated with 0% FBS for 48h, respectively, in Figure 1D. Scale bar, 10 µm. (B) Co-stain of KDM7A and Pol II in Hela cells treated with 0% FBS for 48h. Scale bar, 10 µm. Right, Relative fluorescence intensity of KDM7A and Pol II from a to b. (C) Representative images of KDM7A in Hela cells treated with amino acids starvation for 0h and 48h. Scale bar, 10 µm. (D) The sizes of KDM7A foci in Hela cells under normal and amino acids starvation condition. 16-18 cells were analyzed. ns p>0.05 by unpaired t-test. (E) Representative images of KDM7A in Hela cells treated with 190mM NaCl for 0h and 48h. Scale bar, 10 µm. (F) The sizes of KDM7A foci in Hela cells treated with 190mM NaCl for 0h and 48h. 16-20 cells were analyzed. ****p<0.0001 by unpaired t-test.

Fig.S2: KDM7A condensates in U2OS cells transfected with nGFP-KDM7A. (A) Western blot of H3K9me2 and H3K27me2 in Control and nGFP-KDM7A transfected 293T cells. H3 as the loading control. (B) The localization of nGFP-KDM7A expressed in U2OS cells. Scale bar, 10 µm. (C) The validation of KDM7A antibody. Representative images of immunofluorescence with KDM7A antibody in U2OS cells transfected with nGFP-KDM7A. Right: Relative fluorescence intensity of nGFP-KDM7A and KDM7A antibody from a to b. Scale bar, 10 µm. (D) The separated images of U2OS cells transfected with nGFP-KDM7A and stained with SC35, PSPC1, PML, Coilin, BMI1 and Sam68 in Figure 1E. Scale bar, 10 µm.

Fig. S3: K-bodies interact with proteins associated with important biological processes. (A) Silver staining of SDS-PAGE gel separating proteins immunoprecipitated with GFP-trap in U2OS cells. GFP-only as the negative control. (B) Clustering analysis of nGFP-KDM7A-associated proteins with normalized number of peptides detected by LC-MS. Three biological replicates were conducted for nGFP-KDM7A (K1-K3) and GFP-only (G1-G3), respectively. (C) Ontology (GO) analysis of biological processes of KDM7A-associated proteins in

U2OS cells. The enriched terms are ranked by -log10 (p values). (D) Venn diagram of overlap proteins of KDM7A-associated proteins in Hela cells under 0% FBS and U2OS cells transfected with nGFP-KDM7A.

Fig. S4: KDM7A is partially required for the formation of MCM7 puncta. (A) The localization of KDM7A and HNRNPU in U2OS cells transfected with nGFP-KDM7A. Scale bar, 10 µm. Right, relative fluorescence intensity of KDM7A and HNRNPU from a to b. (B) Co-staining of KDM7A and MCM7 in shControl, shKDM7A-1 and shKDM7A-2 Hela cells treated with 0% FBS for 48h. Scale bar, 10 µm. (C) The relative size of MCM7 foci in shControl, shKDM7A-1 and shKDM7A-2 Hela cells treated with 0% FBS for 48h. 15-16 cells were analyzed. ****p<0.0001 by unpaired t-test. (D) Western blot of KDM7A and MCM7 in shControl Hela cells under 10% FBS and shControl, shKDM7A-1, shKDM7A-2 Hela cells under 0% FBS, respectively. GAPDH as the loading control.

Fig. S5: KDM7A condensates are surrounded by . (A) Representative results of immunofluorescence analysis with H3 antibody in KDM7A transfected (up) and control (down) cell. Scale bar, 10 µm. Right, relative fluorescence intensity of H3 and KDM7A crossed by the arrow on the left.

Fig. S6: K-bodies are formed by LLPS. (A) Schematic representation and representative images of the appearance process of K-bodies in the inducible U2OS cell line. Scale bar, 10 µm. (B) Representative images of U2OS cells transfected with FL or C-terminal nGFP-KDM7A, respectively. Scale bar, 10 µm. (C) Quantification of the number (left) and size (right) of granules formed by FL or C-terminal nGFP-KDM7A. A total of 11 cells about 200 nuclear bodies were counted for each group. *p<0.05, ****p<0.0001 by unpaired t-test. (D) The N-terminal of KDM7A aggregates into the nucleoli as detected by C23 immunofluorescence. Scale bar, 10 µm. (E) A representative fusion event of K-bodies in the U2OS nucleus. Scale bar, 10 µm. (F) FRAP experiments of nGFP-KDM7A in vitro droplets. Left: Representative images of FRAP. Pink box shows the punctum undergoing bleaching, while the blue box shows a control area. Scale bar, 10 µm. Right: Quantification of FRAP data for nGFP-KDM7A droplet. For both bleached area and unbleached control fluorescence intensities are normalized to the pre-bleach intensity. Data are plotted as the mean ± s.d. (n=6). (G) Droplet formation of purified nGFP-C-terminal using different protein concentrations in 75 mM NaCl. Scale bar, 10 µm. (H) Representative images of nGFP-KDM7A droplets by adding 0.25-2 µM DNA (300-700 bp in length). NaCl, 50 mM; nGFP-KDM7A protein, 0.5 µM. Scale bar, 10 µm. (I) FRAP experiment of nGFP-KDM7A in vitro condensates incubated with DNA. Left: Representative images of FRAP. Pink box shows the hollow sphere undergoing bleaching, while the blue box shows a control area. Scale bar, 10 µm. Right: Quantification of FRAP data for nGFP-KDM7A condensates. For both bleached area and unbleached control fluorescence intensities are normalized to the pre-bleach intensity. Data are plotted as the mean ± s.d. (n=6).

Fig. S7: K-bodies exist in vivo. (A) The expression of KDM7A in several mouse tissues detected by western blotting. β-actin as loading control. (B) Immunofluorescence with KDM7A antibody in mouse brain, muscle, and testis tissues. Blue is DAPI and red is endogenous KDM7A. Scale bar, 10 µm. (C) Representative IF images of KDM7A in 12-week-old mouse testis. Round sperms (RS) and elongating sperms (ES) are shown with white arrows. Scale bar, 10 µm. Figure S1 Figure S2 Figure S3 Figure S4 Figure S5 Figure S6 Figure S7 Table S1. KDM7A associated proteins as identified by GFP-trap and mass spectrometry

nGFP-KDM7A (Score) GFP-Only (Score) Accession Description Rep 1 Rep 2 Rep 3 Rep 1 Rep 2 Rep 3 DNA replication licensing factor MCM7 OS=Homo P33993 628.7 721.8 719.1 0.0 0.0 0.0 sapiens GN=MCM7 PE=1 SV=4 - [MCM7_HUMAN] Protein DGCR14 OS=Homo sapiens GN=DGCR14 Q96DF8 371.6 299.1 347.1 0.0 0.0 0.0 PE=1 SV=1 - [DGC14_HUMAN] Proteasome subunit beta type-4 OS=Homo P28070 323.9 243.4 266.6 0.0 0.0 0.0 sapiens GN=PSMB4 PE=1 SV=4 - [PSB4_HUMAN]

ATPase WRNIP1 OS=Homo sapiens GN=WRNIP1 Q96S55 268.4 312.5 253.8 0.0 0.0 0.0 PE=1 SV=2 - [WRIP1_HUMAN] Flap endonuclease 1 OS=Homo sapiens GN=FEN1 P39748 252.8 187.3 132.6 0.0 0.0 0.0 PE=1 SV=1 - [FEN1_HUMAN] Myeloid leukemia factor 2 OS=Homo sapiens Q15773 250.2 174.1 135.8 0.0 0.0 0.0 GN=MLF2 PE=1 SV=1 - [MLF2_HUMAN] Protein MCM10 homolog OS=Homo sapiens Q7L590 232.7 283.1 259.5 0.0 0.0 0.0 GN=MCM10 PE=1 SV=2 - [MCM10_HUMAN] Heat shock protein beta-1 OS=Homo sapiens P04792 231.7 247.8 189.9 0.0 0.0 0.0 GN=HSPB1 PE=1 SV=2 - [HSPB1_HUMAN] Histone-binding protein RBBP7 OS=Homo sapiens Q16576 230.4 211.9 186.9 0.0 0.0 0.0 GN=RBBP7 PE=1 SV=1 - [RBBP7_HUMAN]

Tubulin beta-4B chain OS=Homo sapiens P68371 229.5 290.2 197.0 0.0 0.0 0.0 GN=TUBB4B PE=1 SV=1 - [TBB4B_HUMAN] UBX domain-containing protein 1 OS=Homo Q04323 sapiens GN=UBXN1 PE=1 SV=2 - 221.1 128.3 151.5 0.0 0.0 0.0 [UBXN1_HUMAN] Proteasome subunit beta type-1 OS=Homo P20618 203.5 213.4 178.0 0.0 0.0 0.0 sapiens GN=PSMB1 PE=1 SV=2 - [PSB1_HUMAN] Zinc finger protein 281 OS=Homo sapiens Q9Y2X9 196.3 131.1 162.4 0.0 0.0 0.0 GN=ZNF281 PE=1 SV=1 - [ZN281_HUMAN] Cyclin-dependent inhibitor 2A, isoforms P42771 1/2/3 OS=Homo sapiens GN=CDKN2A PE=1 SV=2 196.1 105.3 38.0 0.0 0.0 0.0 - [CD2A1_HUMAN] RNA -associated protein CTR9 Q6PD62 homolog OS=Homo sapiens GN=CTR9 PE=1 190.1 130.4 109.4 0.0 0.0 0.0 SV=1 - [CTR9_HUMAN]

E3 SUMO-protein PIAS1 OS=Homo sapiens O75925 187.8 139.2 38.2 0.0 0.0 0.0 GN=PIAS1 PE=1 SV=2 - [PIAS1_HUMAN] DnaJ homolog subfamily B member 6 OS=Homo O75190 sapiens GN=DNAJB6 PE=1 SV=2 - 187.6 202.0 138.7 0.0 0.0 0.0 [DNJB6_HUMAN] Cell division control protein 45 homolog OS=Homo O75419 176.4 131.4 129.7 0.0 0.0 0.0 sapiens GN=CDC45 PE=1 SV=1 - [CDC45_HUMAN]

Proteasome subunit alpha type-5 OS=Homo P28066 167.5 106.8 184.2 0.0 0.0 0.0 sapiens GN=PSMA5 PE=1 SV=3 - [PSA5_HUMAN] Cyclin-dependent kinase 1 OS=Homo sapiens P06493 166.5 202.3 216.9 0.0 0.0 0.0 GN=CDK1 PE=1 SV=3 - [CDK1_HUMAN] Transitional endoplasmic reticulum ATPase P55072 OS=Homo sapiens GN=VCP PE=1 SV=4 - 163.4 114.2 45.0 0.0 0.0 0.0 [TERA_HUMAN] Heat shock protein HSP 90-beta OS=Homo P08238 sapiens GN=HSP90AB1 PE=1 SV=4 - 156.5 123.3 88.1 0.0 0.0 0.0 [HS90B_HUMAN] complex protein Nup155 OS=Homo O75694 sapiens GN=NUP155 PE=1 SV=1 - 154.2 90.3 157.1 0.0 0.0 0.0 [NU155_HUMAN]

HEAT repeat-containing protein 2 OS=Homo Q86Y56 sapiens GN=HEATR2 PE=1 SV=4 - 153.3 164.5 118.5 0.0 0.0 0.0 [HEAT2_HUMAN] Proteasome subunit beta type-3 OS=Homo P49720 148.8 102.4 187.1 0.0 0.0 0.0 sapiens GN=PSMB3 PE=1 SV=2 - [PSB3_HUMAN] 26S proteasome non-ATPase regulatory subunit 3 O43242 OS=Homo sapiens GN=PSMD3 PE=1 SV=2 - 145.5 91.1 76.5 0.0 0.0 0.0 [PSMD3_HUMAN] NADH dehydrogenase [ubiquinone] 1 beta O96000 subcomplex subunit 10 OS=Homo sapiens 142.2 105.6 34.9 0.0 0.0 0.0 GN=NDUFB10 PE=1 SV=3 - [NDUBA_HUMAN] Small ubiquitin-related modifier 2 OS=Homo P61956 sapiens GN=SUMO2 PE=1 SV=3 - 137.0 138.7 96.9 0.0 0.0 0.0 [SUMO2_HUMAN] Dual specificity protein phosphatase 9 OS=Homo Q99956 135.7 169.8 76.0 0.0 0.0 0.0 sapiens GN=DUSP9 PE=1 SV=1 - [DUS9_HUMAN]

T-complex protein 1 subunit gamma OS=Homo P49368 127.4 94.2 85.5 0.0 0.0 0.0 sapiens GN=CCT3 PE=1 SV=4 - [TCPG_HUMAN] Replication factor C subunit 1 OS=Homo sapiens P35251 127.4 39.8 65.7 0.0 0.0 0.0 GN=RFC1 PE=1 SV=4 - [RFC1_HUMAN] Testis-specific Y-encoded-like protein 1 OS=Homo Q9H0U9 sapiens GN=TSPYL1 PE=1 SV=3 - 127.3 159.4 122.4 0.0 0.0 0.0 [TSYL1_HUMAN] Homeobox protein Hox-D13 OS=Homo sapiens P35453 124.5 94.6 68.3 0.0 0.0 0.0 GN=HOXD13 PE=1 SV=3 - [HXD13_HUMAN] Telomere length regulation protein TEL2 homolog Q9Y4R8 OS=Homo sapiens GN=TELO2 PE=1 SV=2 - 123.3 139.1 142.5 0.0 0.0 0.0 [TELO2_HUMAN]

Q6PJG6 BRCA1-associated ATM activator 1 OS=Homo 120.7 172.1 123.7 0.0 0.0 0.0 sapiens GN=BRAT1 PE=1 SV=2 - [BRAT1_HUMAN] Annexin A5 OS=Homo sapiens GN=ANXA5 PE=1 P08758 119.0 108.9 88.8 0.0 0.0 0.0 SV=2 - [ANXA5_HUMAN] Non-structural maintenance of Q8WV22 element 1 homolog OS=Homo sapiens 116.7 122.0 87.5 0.0 0.0 0.0 GN=NSMCE1 PE=1 SV=5 - [NSE1_HUMAN] Proteasome subunit beta type-2 OS=Homo P49721 114.2 145.7 106.2 0.0 0.0 0.0 sapiens GN=PSMB2 PE=1 SV=1 - [PSB2_HUMAN]

Uncharacterized protein CXorf57 OS=Homo Q6NSI4 sapiens GN=CXorf57 PE=1 SV=2 - 112.5 70.8 118.6 0.0 0.0 0.0 [CX057_HUMAN] Protein LTV1 homolog OS=Homo sapiens Q96GA3 108.0 55.4 73.3 0.0 0.0 0.0 GN=LTV1 PE=1 SV=1 - [LTV1_HUMAN] component 1 OS=Homo sapiens Q8WXF1 107.8 92.2 27.3 0.0 0.0 0.0 GN=PSPC1 PE=1 SV=1 - [PSPC1_HUMAN] RNA-binding protein PNO1 OS=Homo sapiens Q9NRX1 107.2 102.6 83.0 0.0 0.0 0.0 GN=PNO1 PE=1 SV=1 - [PNO1_HUMAN] T-complex protein 1 subunit alpha OS=Homo P17987 105.6 210.6 166.7 0.0 0.0 0.0 sapiens GN=TCP1 PE=1 SV=1 - [TCPA_HUMAN] BAG family molecular chaperone regulator 2 O95816 OS=Homo sapiens GN=BAG2 PE=1 SV=1 - 104.6 38.3 77.8 0.0 0.0 0.0 [BAG2_HUMAN]

Polyamine-modulated factor 1 OS=Homo sapiens Q6P1K2 102.6 52.9 62.7 0.0 0.0 0.0 GN=PMF1 PE=1 SV=2 - [PMF1_HUMAN] 14-3-3 protein zeta/delta OS=Homo sapiens P63104 102.4 73.6 88.8 0.0 0.0 0.0 GN=YWHAZ PE=1 SV=1 - [1433Z_HUMAN] Lymphoid-specific OS=Homo sapiens Q9NRZ9 101.0 41.5 60.4 0.0 0.0 0.0 GN=HELLS PE=1 SV=1 - [HELLS_HUMAN] Kinesin-like protein KIF23 OS=Homo sapiens Q02241 100.9 58.0 60.1 0.0 0.0 0.0 GN=KIF23 PE=1 SV=3 - [KIF23_HUMAN] Nitric oxide synthase-interacting protein Q9Y314 OS=Homo sapiens GN=NOSIP PE=1 SV=1 - 99.7 106.2 75.6 0.0 0.0 0.0 [NOSIP_HUMAN] G2 and S phase-expressed protein 1 OS=Homo Q9NYZ3 sapiens GN=GTSE1 PE=1 SV=3 - 99.0 74.1 142.5 0.0 0.0 0.0 [GTSE1_HUMAN]

Nucleolar protein 7 OS=Homo sapiens GN=NOL7 Q9UMY1 98.7 68.7 53.0 0.0 0.0 0.0 PE=1 SV=2 - [NOL7_HUMAN] Septin-2 OS=Homo sapiens GN=SEPT2 PE=1 Q15019 98.5 55.0 138.4 0.0 0.0 0.0 SV=1 - [SEPT2_HUMAN] Replication factor C subunit 5 OS=Homo sapiens P40937 98.1 118.5 42.2 0.0 0.0 0.0 GN=RFC5 PE=1 SV=1 - [RFC5_HUMAN] Importin subunit beta-1 OS=Homo sapiens Q14974 97.9 113.5 107.1 0.0 0.0 0.0 GN=KPNB1 PE=1 SV=2 - [IMB1_HUMAN] Endophilin-B1 OS=Homo sapiens GN=SH3GLB1 Q9Y371 95.2 114.7 127.5 0.0 0.0 0.0 PE=1 SV=1 - [SHLB1_HUMAN] BCL-6 corepressor OS=Homo sapiens GN=BCOR Q6W2J9 95.2 44.3 89.4 0.0 0.0 0.0 PE=1 SV=1 - [BCOR_HUMAN] Spectrin beta chain, non-erythrocytic 1 OS=Homo Q01082 sapiens GN=SPTBN1 PE=1 SV=2 - 94.6 136.1 37.9 0.0 0.0 0.0 [SPTB2_HUMAN]

Small ubiquitin-related modifier 3 OS=Homo P55854 sapiens GN=SUMO3 PE=1 SV=2 - 94.5 78.8 106.9 0.0 0.0 0.0 [SUMO3_HUMAN] Sorting nexin-3 OS=Homo sapiens GN=SNX3 O60493 93.7 103.5 22.0 0.0 0.0 0.0 PE=1 SV=3 - [SNX3_HUMAN] B-type OS=Homo sapiens P12277 91.8 199.5 165.7 0.0 0.0 0.0 GN=CKB PE=1 SV=1 - [KCRB_HUMAN] 26S protease regulatory subunit 4 OS=Homo P62191 91.7 91.0 40.7 0.0 0.0 0.0 sapiens GN=PSMC1 PE=1 SV=1 - [PRS4_HUMAN] Coatomer subunit delta OS=Homo sapiens P48444 90.8 82.0 61.6 0.0 0.0 0.0 GN=ARCN1 PE=1 SV=1 - [COPD_HUMAN] Aurora kinase A OS=Homo sapiens GN=AURKA O14965 90.1 70.6 68.4 0.0 0.0 0.0 PE=1 SV=2 - [AURKA_HUMAN]

Polynucleotide 5'-hydroxyl-kinase NOL9 Q5SY16 OS=Homo sapiens GN=NOL9 PE=1 SV=1 - 90.0 41.8 53.4 0.0 0.0 0.0 [NOL9_HUMAN] Histone lysine demethylase PHF8 OS=Homo Q9UPP1 89.1 153.2 272.0 0.0 0.0 0.0 sapiens GN=PHF8 PE=1 SV=3 - [PHF8_HUMAN] Krueppel-like factor 16 OS=Homo sapiens Q9BXK1 87.1 83.3 61.1 0.0 0.0 0.0 GN=KLF16 PE=1 SV=1 - [KLF16_HUMAN] 26S proteasome non-ATPase regulatory subunit O00231 11 OS=Homo sapiens GN=PSMD11 PE=1 SV=3 - 87.1 99.2 70.9 0.0 0.0 0.0 [PSD11_HUMAN] tRNA-splicing endonuclease subunit Sen34 Q9BSV6 OS=Homo sapiens GN=TSEN34 PE=1 SV=1 - 86.3 66.7 69.9 0.0 0.0 0.0 [SEN34_HUMAN] Proteasome subunit alpha type-4 OS=Homo P25789 85.6 86.4 80.0 0.0 0.0 0.0 sapiens GN=PSMA4 PE=1 SV=1 - [PSA4_HUMAN]

Nucleolar protein 9 OS=Homo sapiens GN=NOP9 Q86U38 85.4 75.8 42.7 0.0 0.0 0.0 PE=1 SV=1 - [NOP9_HUMAN] Ribonucleoprotein PTB-binding 1 OS=Homo Q8IY67 sapiens GN=RAVER1 PE=1 SV=1 - 84.9 185.8 151.6 0.0 0.0 0.0 [RAVR1_HUMAN] Homeobox protein SIX1 OS=Homo sapiens Q15475 83.3 122.9 69.2 0.0 0.0 0.0 GN=SIX1 PE=1 SV=1 - [SIX1_HUMAN] D-3-phosphoglycerate dehydrogenase OS=Homo O43175 82.4 37.3 41.4 0.0 0.0 0.0 sapiens GN=PHGDH PE=1 SV=4 - [SERA_HUMAN] T-complex protein 1 subunit eta OS=Homo Q99832 82.0 69.1 21.1 0.0 0.0 0.0 sapiens GN=CCT7 PE=1 SV=2 - [TCPH_HUMAN] DNA-directed RNA I, II, and III P19388 subunit RPABC1 OS=Homo sapiens GN=POLR2E 79.9 94.8 60.1 0.0 0.0 0.0 PE=1 SV=4 - [RPAB1_HUMAN] Small ubiquitin-related modifier 1 OS=Homo P63165 sapiens GN=SUMO1 PE=1 SV=1 - 79.3 79.6 41.7 0.0 0.0 0.0 [SUMO1_HUMAN]

DNA-directed RNA polymerase II subunit Q9GZM3 RPB11-b1 OS=Homo sapiens GN=POLR2J2 PE=1 78.8 69.3 67.1 0.0 0.0 0.0 SV=2 - [RPB1B_HUMAN] DNA replication licensing factor MCM4 OS=Homo P33991 78.8 43.8 40.6 0.0 0.0 0.0 sapiens GN=MCM4 PE=1 SV=5 - [MCM4_HUMAN] Cyclin-dependent kinase inhibitor 2A, isoform 4 Q8N726 OS=Homo sapiens GN=CDKN2A PE=1 SV=2 - 77.7 126.9 149.8 0.0 0.0 0.0 [CD2A2_HUMAN] RRP12-like protein OS=Homo sapiens GN=RRP12 Q5JTH9 77.3 94.1 18.0 0.0 0.0 0.0 PE=1 SV=2 - [RRP12_HUMAN] General transcription factor 3C polypeptide 3 Q9Y5Q9 OS=Homo sapiens GN=GTF3C3 PE=1 SV=1 - 76.4 70.4 63.7 0.0 0.0 0.0 [TF3C3_HUMAN] DNA large subunit OS=Homo sapiens P49643 76.1 39.0 84.1 0.0 0.0 0.0 GN=PRIM2 PE=1 SV=2 - [PRI2_HUMAN]

Protein PML OS=Homo sapiens GN=PML PE=1 P29590 76.1 75.6 62.5 0.0 0.0 0.0 SV=3 - [PML_HUMAN] F-box only protein 7 OS=Homo sapiens Q9Y3I1 75.2 143.8 99.2 0.0 0.0 0.0 GN=FBXO7 PE=1 SV=1 - [FBX7_HUMAN] Cyclin-dependent kinase 4 OS=Homo sapiens P11802 74.5 66.4 42.9 0.0 0.0 0.0 GN=CDK4 PE=1 SV=2 - [CDK4_HUMAN] Phosphomevalonate kinase OS=Homo sapiens Q15126 72.3 68.3 48.0 0.0 0.0 0.0 GN=PMVK PE=1 SV=3 - [PMVK_HUMAN] E3 ubiquitin-protein ligase MARCH7 OS=Homo Q9H992 sapiens GN=MARCH7 PE=1 SV=1 - 72.1 79.1 55.5 0.0 0.0 0.0 [MARH7_HUMAN] Homeobox protein Hox-B9 OS=Homo sapiens P17482 71.4 49.9 62.9 0.0 0.0 0.0 GN=HOXB9 PE=1 SV=2 - [HXB9_HUMAN]

Chromodomain-helicase-DNA-binding protein 8 Q9HCK8 OS=Homo sapiens GN=CHD8 PE=1 SV=5 - 69.2 176.4 125.2 0.0 0.0 0.0 [CHD8_HUMAN] Ribosome-binding protein 1 OS=Homo sapiens Q9P2E9 68.7 59.8 76.6 0.0 0.0 0.0 GN=RRBP1 PE=1 SV=4 - [RRBP1_HUMAN] Dihydrofolate reductase OS=Homo sapiens P00374 68.2 96.4 51.4 0.0 0.0 0.0 GN=DHFR PE=1 SV=2 - [DYR_HUMAN] BRCA2 and CDKN1A-interacting protein OS=Homo Q9P287 68.2 52.0 56.1 0.0 0.0 0.0 sapiens GN=BCCIP PE=1 SV=1 - [BCCIP_HUMAN] Homeobox protein MSX-2 OS=Homo sapiens P35548 68.1 65.6 67.9 0.0 0.0 0.0 GN=MSX2 PE=1 SV=3 - [MSX2_HUMAN] Heterochromatin protein 1-binding protein 3 Q5SSJ5 OS=Homo sapiens GN=HP1BP3 PE=1 SV=1 - 67.1 67.9 49.4 0.0 0.0 0.0 [HP1B3_HUMAN]

Mediator of RNA polymerase II transcription Q6P2C8 subunit 27 OS=Homo sapiens GN=MED27 PE=1 66.4 71.2 63.7 0.0 0.0 0.0 SV=1 - [MED27_HUMAN] 60S ribosomal protein L28 OS=Homo sapiens P46779 66.0 68.6 44.5 0.0 0.0 0.0 GN=RPL28 PE=1 SV=3 - [RL28_HUMAN] Hypoxanthine-guanine phosphoribosyltransferase P00492 OS=Homo sapiens GN=HPRT1 PE=1 SV=2 - 65.4 47.9 104.8 0.0 0.0 0.0 [HPRT_HUMAN] Putative methyltransferase NSUN5 OS=Homo Q96P11 sapiens GN=NSUN5 PE=1 SV=2 - 64.4 39.6 20.4 0.0 0.0 0.0 [NSUN5_HUMAN] 55 kDa erythrocyte membrane protein OS=Homo Q00013 63.7 64.4 35.3 0.0 0.0 0.0 sapiens GN=MPP1 PE=1 SV=2 - [EM55_HUMAN] Phenylalanine--tRNA ligase alpha subunit Q9Y285 OS=Homo sapiens GN=FARSA PE=1 SV=3 - 63.5 103.9 84.5 0.0 0.0 0.0 [SYFA_HUMAN]

Zinc finger CCHC domain-containing protein 10 Q8TBK6 OS=Homo sapiens GN=ZCCHC10 PE=2 SV=1 - 63.1 72.5 49.8 0.0 0.0 0.0 [ZCH10_HUMAN] Kinetochore-associated protein NSL1 homolog Q96IY1 OS=Homo sapiens GN=NSL1 PE=1 SV=3 - 62.4 79.8 54.5 0.0 0.0 0.0 [NSL1_HUMAN] GATA zinc finger domain-containing protein 1 Q8WUU5 OS=Homo sapiens GN=GATAD1 PE=1 SV=1 - 62.2 85.2 63.8 0.0 0.0 0.0 [GATD1_HUMAN] RNA-binding protein NOB1 OS=Homo sapiens Q9ULX3 61.7 80.7 32.2 0.0 0.0 0.0 GN=NOB1 PE=1 SV=1 - [NOB1_HUMAN] Replication protein A 70 kDa DNA-binding subunit P27694 OS=Homo sapiens GN=RPA1 PE=1 SV=2 - 61.6 105.5 44.7 0.0 0.0 0.0 [RFA1_HUMAN] Glutamate-rich protein 1 OS=Homo sapiens Q86X53 60.1 65.1 24.1 0.0 0.0 0.0 GN=ERICH1 PE=1 SV=1 - [ERIC1_HUMAN]

DNA mismatch repair protein Msh6 OS=Homo P52701 59.8 30.3 41.8 0.0 0.0 0.0 sapiens GN=MSH6 PE=1 SV=2 - [MSH6_HUMAN] Pre-mRNA-splicing factor ATP-dependent RNA Q92620 helicase PRP16 OS=Homo sapiens GN=DHX38 59.7 71.7 35.0 0.0 0.0 0.0 PE=1 SV=2 - [PRP16_HUMAN] THO complex subunit 3 OS=Homo sapiens Q96J01 59.6 55.3 52.5 0.0 0.0 0.0 GN=THOC3 PE=1 SV=1 - [THOC3_HUMAN] Acidic leucine-rich nuclear phosphoprotein 32 Q9BTT0 family member E OS=Homo sapiens GN=ANP32E 59.6 81.1 78.1 0.0 0.0 0.0 PE=1 SV=1 - [AN32E_HUMAN] 60S ribosomal protein L31 OS=Homo sapiens P62899 59.6 97.3 43.7 0.0 0.0 0.0 GN=RPL31 PE=1 SV=1 - [RL31_HUMAN]

Proliferating cell nuclear antigen OS=Homo P12004 59.1 44.1 62.6 0.0 0.0 0.0 sapiens GN=PCNA PE=1 SV=1 - [PCNA_HUMAN] Serine/threonine- VRK1 OS=Homo Q99986 58.9 57.2 61.5 0.0 0.0 0.0 sapiens GN=VRK1 PE=1 SV=1 - [VRK1_HUMAN] Nup37 OS=Homo sapiens GN=NUP37 Q8NFH4 58.4 34.6 44.1 0.0 0.0 0.0 PE=1 SV=1 - [NUP37_HUMAN] Lysine-specific demethylase 5B OS=Homo sapiens Q9UGL1 58.0 96.5 75.9 0.0 0.0 0.0 GN=KDM5B PE=1 SV=3 - [KDM5B_HUMAN] E3 ubiquitin-protein ligase UBR5 OS=Homo O95071 57.8 77.2 32.6 0.0 0.0 0.0 sapiens GN=UBR5 PE=1 SV=2 - [UBR5_HUMAN] Bifunctional lysine-specific demethylase and Q8IUF8 histidyl-hydroxylase MINA OS=Homo sapiens 55.9 81.6 77.5 0.0 0.0 0.0 GN=MINA PE=1 SV=1 - [MINA_HUMAN]

60S ribosomal protein L29 OS=Homo sapiens P47914 55.5 61.6 56.9 0.0 0.0 0.0 GN=RPL29 PE=1 SV=2 - [RL29_HUMAN] DCN1-like protein 5 OS=Homo sapiens Q9BTE7 55.0 82.1 73.8 0.0 0.0 0.0 GN=DCUN1D5 PE=1 SV=1 - [DCNL5_HUMAN] Ribonuclease H2 subunit A OS=Homo sapiens O75792 53.7 86.8 111.2 0.0 0.0 0.0 GN=RNASEH2A PE=1 SV=2 - [RNH2A_HUMAN] Tubulin--tyrosine ligase-like protein 12 OS=Homo Q14166 sapiens GN=TTLL12 PE=1 SV=2 - 53.3 60.5 24.8 0.0 0.0 0.0 [TTL12_HUMAN] DnaJ homolog subfamily C member 7 OS=Homo Q99615 sapiens GN=DNAJC7 PE=1 SV=2 - 53.2 44.3 38.9 0.0 0.0 0.0 [DNJC7_HUMAN] Lys-63-specific deubiquitinase BRCC36 OS=Homo P46736 sapiens GN=BRCC3 PE=1 SV=2 - 52.8 103.9 75.0 0.0 0.0 0.0 [BRCC3_HUMAN]

DNA polymerase delta catalytic subunit OS=Homo P28340 sapiens GN=POLD1 PE=1 SV=2 - 52.7 24.7 40.4 0.0 0.0 0.0 [DPOD1_HUMAN] Translation initiation factor eIF-2B subunit beta P49770 OS=Homo sapiens GN=EIF2B2 PE=1 SV=3 - 52.3 78.3 53.7 0.0 0.0 0.0 [EI2BB_HUMAN] Dual specificity protein kinase TTK OS=Homo P33981 51.7 61.7 33.5 0.0 0.0 0.0 sapiens GN=TTK PE=1 SV=2 - [TTK_HUMAN] Probable U3 small nucleolar RNA-associated Q9Y3A2 protein 11 OS=Homo sapiens GN=UTP11L PE=1 51.7 54.4 62.1 0.0 0.0 0.0 SV=2 - [UTP11_HUMAN] Chromatin modification-related protein MEAF6 Q9HAF1 OS=Homo sapiens GN=MEAF6 PE=1 SV=1 - 51.3 71.0 68.3 0.0 0.0 0.0 [EAF6_HUMAN] Polycomb group RING finger protein 1 OS=Homo Q9BSM1 sapiens GN=PCGF1 PE=1 SV=2 - 51.1 72.3 52.9 0.0 0.0 0.0 [PCGF1_HUMAN]

Alpha-actinin-1 OS=Homo sapiens GN=ACTN1 P12814 51.0 43.6 71.6 0.0 0.0 0.0 PE=1 SV=2 - [ACTN1_HUMAN] Thymidylate synthase OS=Homo sapiens P04818 50.9 50.3 88.6 0.0 0.0 0.0 GN=TYMS PE=1 SV=3 - [TYSY_HUMAN] Paired amphipathic helix protein Sin3a OS=Homo Q96ST3 50.9 74.0 24.9 0.0 0.0 0.0 sapiens GN=SIN3A PE=1 SV=2 - [SIN3A_HUMAN] RING finger protein 219 OS=Homo sapiens Q5W0B1 50.5 67.0 43.6 0.0 0.0 0.0 GN=RNF219 PE=1 SV=1 - [RN219_HUMAN] Centromere protein V OS=Homo sapiens Q7Z7K6 49.8 139.9 78.0 0.0 0.0 0.0 GN=CENPV PE=1 SV=1 - [CENPV_HUMAN] 60S ribosomal protein L7-like 1 OS=Homo sapiens Q6DKI1 49.2 50.9 41.4 0.0 0.0 0.0 GN=RPL7L1 PE=1 SV=1 - [RL7L_HUMAN]

60S acidic ribosomal protein P1 OS=Homo sapiens P05386 48.7 48.8 48.7 0.0 0.0 0.0 GN=RPLP1 PE=1 SV=1 - [RLA1_HUMAN] Translin-associated protein X OS=Homo sapiens Q99598 48.2 * 36.4 0.0 0.0 0.0 GN=TSNAX PE=1 SV=1 - [TSNAX_HUMAN] Chromobox protein homolog 2 OS=Homo sapiens Q14781 47.8 47.6 27.0 0.0 0.0 0.0 GN=CBX2 PE=1 SV=2 - [CBX2_HUMAN] Triosephosphate OS=Homo sapiens P60174 47.4 48.5 45.8 0.0 0.0 0.0 GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] V-type proton ATPase subunit E 1 OS=Homo P36543 sapiens GN=ATP6V1E1 PE=1 SV=1 - 47.4 38.1 76.1 0.0 0.0 0.0 [VATE1_HUMAN] Deoxynucleotidyltransferase terminal-interacting Q9H147 protein 1 OS=Homo sapiens GN=DNTTIP1 PE=1 47.0 30.5 85.2 0.0 0.0 0.0 SV=2 - [TDIF1_HUMAN]

Asparagine synthetase [glutamine-hydrolyzing] P08243 OS=Homo sapiens GN=ASNS PE=1 SV=4 - 46.4 39.6 76.6 0.0 0.0 0.0 [ASNS_HUMAN] Methylosome protein 50 OS=Homo sapiens Q9BQA1 46.3 46.2 46.5 0.0 0.0 0.0 GN=WDR77 PE=1 SV=1 - [MEP50_HUMAN] 60S ribosomal protein L9 OS=Homo sapiens P32969 45.8 52.4 36.6 0.0 0.0 0.0 GN=RPL9 PE=1 SV=1 - [RL9_HUMAN] ATP synthase subunit gamma, mitochondrial P36542 OS=Homo sapiens GN=ATP5C1 PE=1 SV=1 - 45.6 56.2 30.6 0.0 0.0 0.0 [ATPG_HUMAN] 7,8-dihydro-8-oxoguanine triphosphatase P36639 OS=Homo sapiens GN=NUDT1 PE=1 SV=3 - 45.4 49.8 45.6 0.0 0.0 0.0 [8ODP_HUMAN] Elongation factor 1-gamma OS=Homo sapiens P26641 45.2 63.4 60.4 0.0 0.0 0.0 GN=EEF1G PE=1 SV=3 - [EF1G_HUMAN] Eukaryotic translation initiation factor 2 subunit 1 P05198 OS=Homo sapiens GN=EIF2S1 PE=1 SV=3 - 45.0 97.5 67.6 0.0 0.0 0.0 [IF2A_HUMAN]

RNA binding protein fox-1 homolog 2 OS=Homo O43251 sapiens GN=RBFOX2 PE=1 SV=3 - 44.0 95.9 65.3 0.0 0.0 0.0 [RFOX2_HUMAN] Origin recognition complex subunit 5 OS=Homo O43913 43.6 70.6 59.2 0.0 0.0 0.0 sapiens GN=ORC5 PE=1 SV=1 - [ORC5_HUMAN] Mannosyl-oligosaccharide glucosidase OS=Homo Q13724 43.5 49.4 58.1 0.0 0.0 0.0 sapiens GN=MOGS PE=1 SV=5 - [MOGS_HUMAN] Toll-interacting protein OS=Homo sapiens Q9H0E2 42.6 42.8 47.3 0.0 0.0 0.0 GN=TOLLIP PE=1 SV=1 - [TOLIP_HUMAN] Spermidine synthase OS=Homo sapiens GN=SRM P19623 42.4 36.8 37.2 0.0 0.0 0.0 PE=1 SV=1 - [SPEE_HUMAN] Integrator complex subunit 11 OS=Homo sapiens Q5TA45 42.4 40.6 45.6 0.0 0.0 0.0 GN=CPSF3L PE=1 SV=2 - [INT11_HUMAN]

Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform OS=Homo Q14738 41.9 37.8 32.7 0.0 0.0 0.0 sapiens GN=PPP2R5D PE=1 SV=1 - [2A5D_HUMAN] Protein FAM115A OS=Homo sapiens Q9Y4C2 41.3 52.6 57.7 0.0 0.0 0.0 GN=FAM115A PE=1 SV=3 - [F115A_HUMAN] Nucleoporin NUP188 homolog OS=Homo sapiens Q5SRE5 41.1 47.4 47.2 0.0 0.0 0.0 GN=NUP188 PE=1 SV=1 - [NU188_HUMAN] E3 ubiquitin-protein ligase RNF169 OS=Homo Q8NCN4 sapiens GN=RNF169 PE=1 SV=2 - 40.6 55.7 39.9 0.0 0.0 0.0 [RN169_HUMAN] Ribosomal RNA small subunit methyltransferase Q92979 NEP1 OS=Homo sapiens GN=EMG1 PE=1 SV=4 - 40.3 62.9 55.2 0.0 0.0 0.0 [NEP1_HUMAN] Probable RNA-binding protein 23 OS=Homo Q86U06 sapiens GN=RBM23 PE=1 SV=1 - 40.2 77.2 64.6 0.0 0.0 0.0 [RBM23_HUMAN]

Phosphoserine aminotransferase OS=Homo Q9Y617 39.4 46.6 32.1 0.0 0.0 0.0 sapiens GN=PSAT1 PE=1 SV=2 - [SERC_HUMAN] Ribosome biogenesis protein BMS1 homolog Q14692 OS=Homo sapiens GN=BMS1 PE=1 SV=1 - 39.2 80.8 50.7 0.0 0.0 0.0 [BMS1_HUMAN] S-phase kinase-associated protein 2 OS=Homo Q13309 39.1 44.5 45.9 0.0 0.0 0.0 sapiens GN=SKP2 PE=1 SV=2 - [SKP2_HUMAN] Zinc phosphodiesterase ELAC protein 2 OS=Homo Q9BQ52 38.6 26.9 53.5 0.0 0.0 0.0 sapiens GN=ELAC2 PE=1 SV=2 - [RNZ2_HUMAN] Nuclear pore complex protein Nup160 OS=Homo Q12769 sapiens GN=NUP160 PE=1 SV=3 - 38.3 26.0 45.0 0.0 0.0 0.0 [NU160_HUMAN]

Actin-related protein 2 OS=Homo sapiens P61160 38.1 52.5 53.2 0.0 0.0 0.0 GN=ACTR2 PE=1 SV=1 - [ARP2_HUMAN] Nucleolar complex protein 3 homolog OS=Homo Q8WTT2 sapiens GN=NOC3L PE=1 SV=1 - 37.0 52.5 52.6 0.0 0.0 0.0 [NOC3L_HUMAN] Chromatin assembly factor 1 subunit B OS=Homo Q13112 sapiens GN=CHAF1B PE=1 SV=1 - 33.9 51.7 58.1 0.0 0.0 0.0 [CAF1B_HUMAN] Gem-associated protein 4 OS=Homo sapiens P57678 33.4 70.8 40.1 0.0 0.0 0.0 GN=GEMIN4 PE=1 SV=2 - [GEMI4_HUMAN] Ribosome biogenesis protein NSA2 homolog O95478 OS=Homo sapiens GN=NSA2 PE=1 SV=1 - 33.1 62.7 61.8 0.0 0.0 0.0 [NSA2_HUMAN] Plakophilin-2 OS=Homo sapiens GN=PKP2 PE=1 Q99959 32.7 61.4 40.5 0.0 0.0 0.0 SV=2 - [PKP2_HUMAN]

26S protease regulatory subunit 6A OS=Homo P17980 sapiens GN=PSMC3 PE=1 SV=3 - 32.4 23.4 60.9 0.0 0.0 0.0 [PRS6A_HUMAN] 28S ribosomal protein S34, mitochondrial P82930 OS=Homo sapiens GN=MRPS34 PE=1 SV=2 - 31.8 42.8 38.9 0.0 0.0 0.0 [RT34_HUMAN] E3 ubiquitin-protein ligase TRIP12 OS=Homo Q14669 sapiens GN=TRIP12 PE=1 SV=1 - 31.8 73.1 74.4 0.0 0.0 0.0 [TRIPC_HUMAN] Tonsoku-like protein OS=Homo sapiens Q96HA7 30.9 25.7 82.8 0.0 0.0 0.0 GN=TONSL PE=1 SV=2 - [TONSL_HUMAN] Armadillo repeat-containing protein 6 OS=Homo Q6NXE6 sapiens GN=ARMC6 PE=1 SV=2 - 30.9 78.0 123.1 0.0 0.0 0.0 [ARMC6_HUMAN] Cleavage and specificity factor Q9UKF6 subunit 3 OS=Homo sapiens GN=CPSF3 PE=1 30.3 25.6 46.3 0.0 0.0 0.0 SV=1 - [CPSF3_HUMAN]

Proline-rich protein 14 OS=Homo sapiens Q9BWN1 29.5 52.0 38.5 0.0 0.0 0.0 GN=PRR14 PE=1 SV=1 - [PRR14_HUMAN] General transcription factor 3C polypeptide 1 Q12789 OS=Homo sapiens GN=GTF3C1 PE=1 SV=4 - 28.6 79.8 38.7 0.0 0.0 0.0 [TF3C1_HUMAN] hormone receptor ERR1 OS=Homo P11474 28.0 24.8 43.1 0.0 0.0 0.0 sapiens GN=ESRRA PE=1 SV=3 - [ERR1_HUMAN] ATP-dependent DNA helicase Q4 OS=Homo O94761 sapiens GN=RECQL4 PE=1 SV=1 - 27.7 32.9 28.0 0.0 0.0 0.0 [RECQ4_HUMAN] Ester C11orf54 OS=Homo sapiens Q9H0W9 27.0 23.9 21.0 0.0 0.0 0.0 GN=C11orf54 PE=1 SV=1 - [CK054_HUMAN]

Actin-related protein 2/3 complex subunit 3 O15145 OS=Homo sapiens GN=ARPC3 PE=1 SV=3 - 26.5 88.4 24.6 0.0 0.0 0.0 [ARPC3_HUMAN] Ribonuclease P protein subunit p29 OS=Homo O95707 25.3 25.6 27.8 0.0 0.0 0.0 sapiens GN=POP4 PE=1 SV=2 - [RPP29_HUMAN] Ribonucleases P/MRP protein subunit POP1 Q99575 OS=Homo sapiens GN=POP1 PE=1 SV=2 - 24.3 30.0 66.2 0.0 0.0 0.0 [POP1_HUMAN] Akirin-2 OS=Homo sapiens GN=AKIRIN2 PE=1 Q53H80 21.7 33.3 27.1 0.0 0.0 0.0 SV=2 - [AKIR2_HUMAN] Thioredoxin-interacting protein OS=Homo sapiens Q9H3M7 21.7 60.5 54.5 0.0 0.0 0.0 GN=TXNIP PE=1 SV=1 - [TXNIP_HUMAN] E3 ubiquitin-protein ligase UHRF1 OS=Homo Q96T88 sapiens GN=UHRF1 PE=1 SV=1 - 181.3 192.4 146.1 137.4 0.0 0.0 [UHRF1_HUMAN]

Myb-binding protein 1A OS=Homo sapiens Q9BQG0 148.0 348.2 246.4 78.8 0.0 0.0 GN=MYBBP1A PE=1 SV=2 - [MBB1A_HUMAN] Testis-expressed sequence 10 protein OS=Homo Q9NXF1 102.4 100.5 57.9 67.3 0.0 0.0 sapiens GN=TEX10 PE=1 SV=2 - [TEX10_HUMAN] F-actin-capping protein subunit alpha-2 OS=Homo P47755 sapiens GN=CAPZA2 PE=1 SV=3 - 68.8 53.1 58.8 62.4 0.0 0.0 [CAZA2_HUMAN] Bromodomain adjacent to zinc finger domain Q9NRL2 protein 1A OS=Homo sapiens GN=BAZ1A PE=1 54.7 139.0 107.4 59.5 0.0 0.0 SV=2 - [BAZ1A_HUMAN] Exosome complex component MTR3 OS=Homo Q5RKV6 sapiens GN=EXOSC6 PE=1 SV=1 - 39.5 43.1 50.6 53.7 0.0 0.0 [EXOS6_HUMAN] Ribosomal RNA processing protein 1 homolog A P56182 OS=Homo sapiens GN=RRP1 PE=1 SV=1 - 71.7 65.6 147.7 46.2 0.0 0.0 [RRP1_HUMAN]

THAP domain-containing protein 11 OS=Homo Q96EK4 sapiens GN=THAP11 PE=1 SV=2 - 66.5 70.4 57.2 40.9 0.0 0.0 [THA11_HUMAN] Mitotic spindle assembly checkpoint protein Q13257 MAD2A OS=Homo sapiens GN=MAD2L1 PE=1 32.2 96.0 68.0 32.5 0.0 0.0 SV=1 - [MD2L1_HUMAN] Proline-, glutamic acid- and leucine-rich protein 1 Q8IZL8 OS=Homo sapiens GN=PELP1 PE=1 SV=2 - 98.3 140.9 61.5 29.3 0.0 0.0 [PELP1_HUMAN] Probable RNA-binding protein 19 OS=Homo Q9Y4C8 sapiens GN=RBM19 PE=1 SV=3 - 33.4 81.3 98.5 26.6 0.0 0.0 [RBM19_HUMAN] Nuclear pore complex protein Nup205 OS=Homo Q92621 sapiens GN=NUP205 PE=1 SV=3 - 58.0 61.2 40.9 25.7 0.0 0.0 [NU205_HUMAN]

Protein arginine N-methyltransferase 5 OS=Homo O14744 sapiens GN=PRMT5 PE=1 SV=4 - 21.5 75.7 24.7 0.0 0.0 0.0 [ANM5_HUMAN] Heterogeneous nuclear ribonucleoprotein H2 P55795 OS=Homo sapiens GN=HNRNPH2 PE=1 SV=1 - 426.3 384.7 486.9 0.0 213.8 0.0 [HNRH2_HUMAN] Serine/arginine-rich splicing factor 4 OS=Homo Q08170 78.6 75.9 122.5 0.0 179.5 0.0 sapiens GN=SRSF4 PE=1 SV=2 - [SRSF4_HUMAN] TAR DNA-binding protein 43 OS=Homo sapiens Q13148 90.2 190.4 189.2 0.0 104.5 0.0 GN=TARDBP PE=1 SV=1 - [TADBP_HUMAN] Eukaryotic translation initiation factor 3 subunit L Q9Y262 OS=Homo sapiens GN=EIF3L PE=1 SV=1 - 117.0 110.5 134.7 0.0 101.9 0.0 [EIF3L_HUMAN] Eukaryotic translation initiation factor 3 subunit F O00303 OS=Homo sapiens GN=EIF3F PE=1 SV=1 - 39.3 88.6 105.9 0.0 81.0 0.0 [EIF3F_HUMAN]

MKI67 FHA domain-interacting nucleolar Q9BYG3 phosphoprotein OS=Homo sapiens GN=NIFK 182.4 216.6 195.6 0.0 79.4 0.0 PE=1 SV=1 - [MK67I_HUMAN] WD repeat-containing protein 74 OS=Homo Q6RFH5 sapiens GN=WDR74 PE=1 SV=1 - 109.4 98.7 81.2 0.0 66.3 0.0 [WDR74_HUMAN] Mitochondrial ribonuclease P protein 1 OS=Homo Q7L0Y3 sapiens GN=TRMT10C PE=1 SV=2 - 111.6 142.1 68.1 0.0 59.2 0.0 [MRRP1_HUMAN] RNA-binding protein 10 OS=Homo sapiens P98175 53.4 93.6 119.7 0.0 58.9 0.0 GN=RBM10 PE=1 SV=3 - [RBM10_HUMAN] Nucleolar MIF4G domain-containing protein 1 Q5C9Z4 OS=Homo sapiens GN=NOM1 PE=1 SV=1 - 55.0 38.7 47.1 0.0 53.7 0.0 [NOM1_HUMAN] Glutamate-rich WD repeat-containing protein 1 Q9BQ67 85.0 49.1 65.2 0.0 50.4 0.0 OS=Homo sapiens GN=GRWD1 PE=1 SV=1 - [GRWD1_HUMAN]

Transcription factor A, mitochondrial OS=Homo Q00059 48.2 23.6 39.5 0.0 49.7 0.0 sapiens GN=TFAM PE=1 SV=1 - [TFAM_HUMAN] Replication factor C subunit 2 OS=Homo sapiens P35250 21.2 69.4 44.0 0.0 49.0 0.0 GN=RFC2 PE=1 SV=3 - [RFC2_HUMAN] Telomere-associated protein RIF1 OS=Homo Q5UIP0 32.1 38.6 74.6 0.0 48.8 0.0 sapiens GN=RIF1 PE=1 SV=2 - [RIF1_HUMAN]

U3 small nucleolar ribonucleoprotein protein IMP3 Q9NV31 OS=Homo sapiens GN=IMP3 PE=1 SV=1 - 65.8 30.1 117.6 0.0 47.5 0.0 [IMP3_HUMAN] Probable ATP-dependent RNA helicase DDX49 Q9Y6V7 OS=Homo sapiens GN=DDX49 PE=1 SV=1 - 85.4 73.0 50.1 0.0 44.7 0.0 [DDX49_HUMAN] 40S ribosomal protein S10 OS=Homo sapiens P46783 134.3 212.3 230.3 0.0 43.4 0.0 GN=RPS10 PE=1 SV=1 - [RS10_HUMAN] Nuclear valosin-containing protein-like OS=Homo O15381 181.7 239.9 251.3 0.0 39.5 0.0 sapiens GN=NVL PE=1 SV=1 - [NVL_HUMAN] WD repeat-containing protein 75 OS=Homo Q8IWA0 sapiens GN=WDR75 PE=1 SV=1 - 125.7 189.0 191.3 0.0 38.0 0.0 [WDR75_HUMAN] THO complex subunit 6 homolog OS=Homo Q86W42 sapiens GN=THOC6 PE=1 SV=1 - 91.6 136.5 142.0 0.0 37.5 0.0 [THOC6_HUMAN]

Nucleoporin p54 OS=Homo sapiens GN=NUP54 Q7Z3B4 23.9 34.8 31.3 0.0 37.5 0.0 PE=1 SV=2 - [NUP54_HUMAN] Superkiller viralicidic activity 2-like 2 OS=Homo P42285 sapiens GN=SKIV2L2 PE=1 SV=3 - 89.7 60.6 61.0 0.0 36.8 0.0 [SK2L2_HUMAN] SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily Q969G3 90.7 50.7 60.0 0.0 36.7 0.0 E member 1 OS=Homo sapiens GN=SMARCE1 PE=1 SV=2 - [SMCE1_HUMAN] U3 small nucleolar ribonucleoprotein protein O00566 MPP10 OS=Homo sapiens GN=MPHOSPH10 PE=1 49.7 112.9 89.9 0.0 34.8 0.0 SV=2 - [MPP10_HUMAN] Regulation of nuclear pre-mRNA Q96P16 domain-containing protein 1A OS=Homo sapiens 123.5 77.5 48.0 0.0 34.7 0.0 GN=RPRD1A PE=1 SV=1 - [RPR1A_HUMAN] PIN2/TERF1-interacting inhibitor 1 Q96BK5 OS=Homo sapiens GN=PINX1 PE=1 SV=2 - 25.2 40.7 38.2 0.0 34.5 0.0 [PINX1_HUMAN]

40S ribosomal protein S15 OS=Homo sapiens P62841 62.5 108.9 39.3 0.0 33.6 0.0 GN=RPS15 PE=1 SV=2 - [RS15_HUMAN] Nucleoporin Nup43 OS=Homo sapiens GN=NUP43 Q8NFH3 79.3 29.7 110.5 0.0 32.1 0.0 PE=1 SV=1 - [NUP43_HUMAN] Ribonuclease P protein subunit p20 OS=Homo O75817 67.2 62.5 83.3 0.0 32.0 0.0 sapiens GN=POP7 PE=1 SV=2 - [POP7_HUMAN] Eukaryotic translation initiation factor 3 subunit E P60228 OS=Homo sapiens GN=EIF3E PE=1 SV=1 - 231.0 304.8 210.2 0.0 30.2 0.0 [EIF3E_HUMAN] Zinc finger protein ubi-d4 OS=Homo sapiens Q92785 62.7 126.8 156.5 0.0 28.9 0.0 GN=DPF2 PE=1 SV=2 - [REQU_HUMAN]

Protein LSM14 homolog B OS=Homo sapiens Q9BX40 20.4 44.7 56.8 0.0 27.7 0.0 GN=LSM14B PE=1 SV=1 - [LS14B_HUMAN] Nucleolar complex protein 2 homolog OS=Homo Q9Y3T9 sapiens GN=NOC2L PE=1 SV=4 - 71.1 70.0 85.6 0.0 25.8 0.0 [NOC2L_HUMAN] DNA replication licensing factor MCM2 OS=Homo P49736 53.8 64.2 54.0 0.0 25.7 0.0 sapiens GN=MCM2 PE=1 SV=4 - [MCM2_HUMAN] Nuclear pore complex protein Nup133 OS=Homo Q8WUM0 sapiens GN=NUP133 PE=1 SV=2 - 343.3 368.1 146.5 0.0 25.6 0.0 [NU133_HUMAN] tRNA (cytosine(34)-C(5))-methyltransferase Q08J23 OS=Homo sapiens GN=NSUN2 PE=1 SV=2 - 168.1 118.1 61.6 0.0 21.8 0.0 [NSUN2_HUMAN] Lysine-specific demethylase 7A OS=Homo sapiens Q6ZMT4 1678.6 1955.0 1401.1 0.0 0.0 129.5 GN=KDM7A PE=1 SV=2 - [KDM7A_HUMAN]

Structural maintenance of chromosomes protein Q14683 1A OS=Homo sapiens GN=SMC1A PE=1 SV=2 - 32.0 96.5 43.7 0.0 0.0 72.0 [SMC1A_HUMAN] FACT complex subunit SPT16 OS=Homo sapiens Q9Y5B9 77.2 163.4 110.6 0.0 0.0 50.4 GN=SUPT16H PE=1 SV=1 - [SP16H_HUMAN] Structural maintenance of chromosomes protein 3 Q9UQE7 OS=Homo sapiens GN=SMC3 PE=1 SV=2 - 118.5 190.6 38.2 0.0 0.0 43.3 [SMC3_HUMAN] FACT complex subunit SSRP1 OS=Homo sapiens Q08945 345.5 342.2 211.4 0.0 0.0 37.4 GN=SSRP1 PE=1 SV=1 - [SSRP1_HUMAN] Eukaryotic translation initiation factor 3 subunit K Q9UBQ5 OS=Homo sapiens GN=EIF3K PE=1 SV=1 - 64.4 100.3 57.8 0.0 0.0 36.1 [EIF3K_HUMAN] Guanine nucleotide-binding protein subunit P63244 beta-2-like 1 OS=Homo sapiens GN=GNB2L1 381.0 321.9 206.5 0.0 0.0 32.6 PE=1 SV=3 - [GBLP_HUMAN]

THO complex subunit 2 OS=Homo sapiens Q8NI27 88.0 104.1 87.4 0.0 0.0 32.3 GN=THOC2 PE=1 SV=2 - [THOC2_HUMAN] A-kinase anchor protein 8-like OS=Homo sapiens Q9ULX6 53.1 61.6 38.4 0.0 0.0 31.8 GN=AKAP8L PE=1 SV=3 - [AKP8L_HUMAN] Protein FRG1 OS=Homo sapiens GN=FRG1 PE=1 Q14331 49.6 38.6 42.7 0.0 0.0 29.1 SV=1 - [FRG1_HUMAN] KRR1 small subunit processome component Q13601 homolog OS=Homo sapiens GN=KRR1 PE=1 55.7 35.4 66.4 0.0 0.0 26.4 SV=4 - [KRR1_HUMAN] DNA-directed RNA polymerase I subunit RPA49 Q9GZS1 OS=Homo sapiens GN=POLR1E PE=1 SV=2 - 123.9 132.1 96.9 0.0 0.0 25.8 [RPA49_HUMAN] Endonuclease III-like protein 1 OS=Homo sapiens P78549 113.0 97.2 44.0 0.0 0.0 23.9 GN=NTHL1 PE=1 SV=2 - [NTHL1_HUMAN]

Atherin OS=Homo sapiens GN=SAMD1 PE=1 Q6SPF0 30.6 41.4 61.5 0.0 0.0 20.3 SV=1 - [SAMD1_HUMAN] Protein arginine N-methyltransferase 5 OS=Homo O14744 sapiens GN=PRMT5 PE=1 SV=4 - 21.5 75.7 24.7 0.0 0.0 0.0 [ANM5_HUMAN] Table S2. Proteome of endogenous KDM7A in Hela cells under 0% FBS condition

KDM7A (iBAQ) IgG (iBAQ) Accession Description Rep 1 Rep 2 Rep 3 Rep 1 Rep 2 Rep 3 P10412 H14_HUMAN Histone H1.4 12981000 25846000 14598000 0 0 0

Q99878 H2A1J_HUMAN Histone H2A type 1-J 11121000 897460 0 0 0 0

Q92686 NEUG_HUMAN Neurogranin 10055000 10260000 0 0 0 0 RL40_HUMAN Ubiquitin-60S ribosomal P62987 9890700 15897000 20985000 3995800 0 0 protein L40

HNRPC_HUMAN Heterogeneous nuclear P07910 7002700 12954000 10341000 0 0 0 ribonucleoproteins C1/C2

Q96PK6 RBM14_HUMAN RNA-binding protein 14 5848100 6722400 5850000 157110 0 0

Q99880 H2B1L_HUMAN Histone H2B type 1-L 5511000 2190900 2606700 5764300 0 0

ROA1_HUMAN Heterogeneous nuclear P09651 5161500 13559000 9240700 0 0 0 ribonucleoprotein A1

P35579 MYH9_HUMAN Myosin-9 5094400 10264000 6130600 0 0 0 RBMX_HUMAN RNA-binding motif protein, P38159 4931600 7996700 5255500 0 0 0 X

O75367 H2AY_HUMAN Core histone macro-H2A.1 4568900 17588000 5852000 0 0 0

P07305 H10_HUMAN Histone H1.0 4558500 9918600 26612000 0 0 0 P02545 LMNA_HUMAN Prelamin-A/C 3865300 5679300 2757800 0 62354 0 HNRPM_HUMAN Heterogeneous nuclear P52272 3738600 4523400 2154400 0 0 0 ribonucleoprotein M IF4A1_HUMAN Eukaryotic initiation factor P60842 3321300 4577500 2819600 0 0 0 4A-I HNRPU_HUMAN Heterogeneous nuclear Q00839 3210400 10499000 7112200 328200 0 0 ribonucleoprotein U

P06748 NPM_HUMAN Nucleophosmin 3069600 0 2902900 238410 0 0 ROA2_HUMAN Heterogeneous nuclear P22626 2632500 8189500 3749500 0 0 0 ribonucleoproteins A2/B1 FBRL_HUMAN rRNA 2-O-methyltransferase P22087 2572300 3485000 2447900 0 0 0 fibrillarin

P05141 ADT2_HUMAN ADP/ATP 2 2528600 3051900 2929900 0 0 0

Q92522 H1X_HUMAN Histone H1x 2353400 7508800 5010200 0 0 0 HNRPF_HUMAN Heterogeneous nuclear P52597 2316800 2876000 4900700 0 0 0 ribonucleoprotein F P81605 DCD_HUMAN Dermcidin 2131900 0 1191600 28171000 0 0 DHX9_HUMAN ATP-dependent RNA Q08211 1851100 2681100 1838700 0 0 0 helicase A

DDX5_HUMAN Probable ATP-dependent P17844 1746200 1049600 1283300 0 0 0 RNA helicase DDX5

P11021 BIP_HUMAN Endoplasmic reticulum 1682100 2940000 2123600 0 0 0 chaperone BiP

Q9NR30 DDX21_HUMAN Nucleolar RNA helicase 2 1669200 3146200 2148900 0 0 0

NOP2_HUMAN Probable 28S rRNA P46087 1652900 2586300 2161600 0 0 0 (cytosine(4447)-C(5))-methyltransferase PARP1_HUMAN Poly [ADP-ribose] P09874 1620600 4164300 3075700 0 0 0 polymerase 1 HS90B_HUMAN Heat shock protein HSP P08238 1495100 2108400 783220 0 0 0 90-beta ILF2_HUMAN Interleukin enhancer-binding Q12905 1278800 2057500 1163500 0 0 0 factor 2

P06493 CDK1_HUMAN Cyclin-dependent kinase 1 1253800 1227100 1182800 0 0 0

SRBS2_HUMAN Sorbin and SH3 O94875 1232400 1767400 1078900 0 0 0 domain-containing protein 2 NUMA1_HUMAN Nuclear mitotic apparatus Q14980 1146700 2290100 1056400 0 0 0 protein 1 P12814 ACTN1_HUMAN Alpha-actinin-1 1066100 1868900 956870 0 0 0

HNRH2_HUMAN Heterogeneous nuclear P55795 1038300 1841300 1158100 0 0 0 ribonucleoprotein H2 DDX3X_HUMAN ATP-dependent RNA O00571 1034000 2184500 685990 53961 0 0 helicase DDX3X HNRPK_HUMAN Heterogeneous nuclear P61978 987300 1308200 1064800 0 87690 0 ribonucleoprotein K IF6_HUMAN Eukaryotic translation P56537 964350 1538900 666790 0 0 0 initiation factor 6 DHB4_HUMAN Peroxisomal multifunctional P51659 963630 722320 813210 0 0 0 type 2

O00567 NOP56_HUMAN Nucleolar protein 56 872250 2046800 727370 0 0 0

O43795 MYO1B_HUMAN Unconventional myosin-Ib 855070 1599600 942190 0 0 0

P26373 RL13_HUMAN 60S ribosomal protein L13 851040 464890 508890 0 0 0

TOP2A_HUMAN DNA topoisomerase P11388 837090 1206800 939260 0 0 0 2-alpha P35580 MYH10_HUMAN Myosin-10 826690 2511700 756860 0 0 0 G3P_HUMAN Glyceraldehyde-3-phosphate P04406 809270 5008400 745850 1654400 0 0 dehydrogenase

P62917 RL8_HUMAN 60S ribosomal protein L8 804450 2850700 1108700 0 0 0

RS4X_HUMAN 40S ribosomal protein S4, X P62701 789750 1503100 912730 0 0 0 isoform P19338 NUCL_HUMAN Nucleolin 756760 1246900 721610 0 0 0

LIMA1_HUMAN LIM domain and Q9UHB6 745710 590600 428520 0 0 0 actin-binding protein 1

Q8IVT2 MISP_HUMAN Mitotic interactor and 738490 601530 324070 0 0 0 substrate of PLK1

GRP75_HUMAN Stress-70 protein, P38646 737090 792390 313880 62317 0 0 mitochondrial EBP2_HUMAN Probable rRNA-processing Q99848 734100 488260 1046400 0 0 0 protein EBP2 CAZA2_HUMAN F-actin-capping protein P47755 697960 471470 90748 0 0 0 subunit alpha-2

Q15717 ELAV1_HUMAN ELAV-like protein 1 682340 1084300 533820 0 0 0

HP1B3_HUMAN Heterochromatin protein Q5SSJ5 658280 1231700 892030 0 0 0 1-binding protein 3 HS71B_HUMAN Heat shock 70 kDa protein P0DMV9 634460 641230 525760 0 0 0 1B P14625 ENPL_HUMAN Endoplasmin 624250 2330200 878970 0 0 0

MIC60_HUMAN MICOS complex subunit Q16891 620730 1015200 591350 0 0 0 MIC60

P0CW18 PRS56_HUMAN Serine protease 56 597440 1147100 959020 0 0 0

IMDH2_HUMAN Inosine-5-monophosphate P12268 593720 961400 627150 40603 0 0 dehydrogenase 2 Q99959 PKP2_HUMAN Plakophilin-2 593550 1138100 598210 0 0 0 P08254 MMP3_HUMAN Stromelysin-1 590910 0 1174400 0 0 2230500 HNRPL_HUMAN Heterogeneous nuclear P14866 586160 1137100 229110 0 0 0 ribonucleoprotein L O95425 SVIL_HUMAN Supervillin 582240 689260 514740 0 0 0 P13639 EF2_HUMAN Elongation factor 2 521000 1215000 622900 42152 0 0

Q86V81 THOC4_HUMAN THO complex subunit 4 515590 2007200 1047900 0 0 0

SPTN1_HUMAN Spectrin alpha chain, Q13813 510720 642220 533130 0 0 0 non-erythrocytic 1

ILF3_HUMAN Interleukin enhancer-binding Q12906 502400 1450200 515350 0 0 0 factor 3 GSTM5_HUMAN Glutathione S- P46439 494670 792390 548480 0 0 0 Mu 5 SERA_HUMAN D-3-phosphoglycerate O43175 493030 269050 122910 0 0 0 dehydrogenase

P62753 RS6_HUMAN 40S ribosomal protein S6 473720 1290900 444990 0 0 0

SPTB2_HUMAN Spectrin beta chain, Q01082 465340 527650 464960 0 0 0 non-erythrocytic 1 PP1B_HUMAN Serine/threonine-protein P62140 448060 771030 446180 0 0 0 phosphatase PP1-beta catalytic subunit CAZA1_HUMAN F-actin-capping protein P52907 443400 944790 562000 0 0 0 subunit alpha-1 CCD86_HUMAN Coiled-coil Q9H6F5 440520 3090600 1625500 0 0 0 domain-containing protein 86 Q15366 PCBP2_HUMAN Poly(rC)-binding protein 2 435350 1565200 534450 0 0 0

P11387 TOP1_HUMAN DNA topoisomerase 1 428420 937900 441790 0 0 0

YBOX1_HUMAN Nuclease-sensitive P67809 424210 673190 208140 0 0 0 element-binding protein 1 CH60_HUMAN 60 kDa heat shock protein, P10809 419180 618070 454140 0 0 0 mitochondrial ROA3_HUMAN Heterogeneous nuclear P51991 408390 2778100 2101500 0 0 0 ribonucleoprotein A3 P43243 MATR3_HUMAN Matrin-3 400970 1326800 899710 0 0 0 KI67_HUMAN Proliferation marker protein P46013 390170 620150 608040 0 0 0 Ki-67 ATD3A_HUMAN ATPase family AAA Q9NVI7 384250 966670 739470 0 0 0 domain-containing protein 3A

IF4A3_HUMAN Eukaryotic initiation factor P38919 375300 427610 443050 0 0 0 4A-III SRSF1_HUMAN Serine/arginine-rich Q07955 370500 736780 584720 0 0 0 splicing factor 1

P14923 PLAK_HUMAN Junction plakoglobin 366990 689140 437010 729120 0 0

BRX1_HUMAN Ribosome biogenesis Q8TDN6 352670 750450 467240 0 0 0 protein BRX1 homolog BAG2_HUMAN BAG family molecular O95816 350300 1150700 994760 0 0 0 chaperone regulator 2 P49327 FAS_HUMAN Fatty acid synthase 348800 490960 356980 0 0 0 Q14126 DSG2_HUMAN Desmoglein-2 339700 446200 222550 0 0 0 HCD2_HUMAN 3-hydroxyacyl-CoA Q99714 323800 278710 0 0 0 0 dehydrogenase type-2

GSTK1_HUMAN Glutathione S-transferase Q9Y2Q3 321720 432830 412170 0 0 0 kappa 1 NONO_HUMAN Non-POU Q15233 domain-containing octamer-binding 308150 701930 833170 0 0 0 protein

P39023 RL3_HUMAN 60S ribosomal protein L3 303580 551740 347760 0 0 0

PGAM5_HUMAN Serine/threonine-protein Q96HS1 294760 598400 287740 0 0 0 phosphatase PGAM5, mitochondrial

NAT10_HUMAN RNA cytidine Q9H0A0 290930 414670 181750 0 0 0 acetyltransferase MCM7_HUMAN DNA replication licensing P33993 285510 444920 112960 0 0 0 factor MCM7

LPPRC_HUMAN Leucine-rich PPR P42704 276800 285700 308670 0 0 0 motif-containing protein, mitochondrial DHX15_HUMAN Pre-mRNA-splicing factor O43143 276420 764680 182600 0 0 0 ATP-dependent RNA helicase DHX15 Q8N3V7 SYNPO_HUMAN Synaptopodin 274180 654250 267410 0 0 0 MIC19_HUMAN MICOS complex subunit Q9NX63 272850 1678400 292260 0 0 0 MIC19

P14618 KPYM_HUMAN PKM 267910 480670 260510 0 0 0

PDIP3_HUMAN Polymerase Q9BY77 265270 591620 93358 0 0 0 delta-interacting protein 3 RACK1_HUMAN Receptor of activated P63244 256680 411430 119620 0 0 0 protein C kinase 1 SRSF7_HUMAN Serine/arginine-rich Q16629 248160 341030 288400 0 0 0 splicing factor 7

XRCC6_HUMAN X-ray repair P12956 237240 479370 266730 0 0 0 cross-complementing protein 6 P35659 DEK_HUMAN Protein DEK 230500 1419600 258250 0 0 0 P66B_HUMAN Transcriptional repressor Q8WXI9 226790 120590 190040 0 0 0 p66-beta

Q14974 IMB1_HUMAN Importin subunit beta-1 226490 257790 0 0 0 0

C1TC_HUMAN C-1-tetrahydrofolate P11586 225720 390040 229830 0 0 0 synthase, cytoplasmic G3BP2_HUMAN Ras GTPase-activating Q9UN86 225070 231610 0 0 0 0 protein-binding protein 2

Q9BQG0 MBB1A_HUMAN Myb-binding protein 1A 215310 245560 315860 0 0 0

RFC3_HUMAN Replication factor C subunit P40938 213400 255320 266360 0 0 0 3

P43405 KSYK_HUMAN Tyrosine-protein kinase SYK 211470 0 344830 0 0 0

HSDL2_HUMAN Hydroxysteroid Q6YN16 209800 414480 190640 0 0 0 dehydrogenase-like protein 2 SRRM2_HUMAN Serine/arginine repetitive Q9UQ35 204580 324720 196070 0 0 0 matrix protein 2 DNJA1_HUMAN DnaJ homolog subfamily A P31689 204150 228420 201070 0 0 0 member 1

P21333 FLNA_HUMAN Filamin-A 199990 257820 210820 0 0 0 HNRPD_HUMAN Heterogeneous nuclear Q14103 198000 378980 281940 0 0 0 ribonucleoprotein D0

Q02878 RL6_HUMAN 60S ribosomal protein L6 195910 674170 390550 0 0 0

Q9NYL9 TMOD3_HUMAN Tropomodulin-3 189570 495740 351810 0 0 0 SMCA5_HUMAN SWI/SNF-related matrix-associated actin-dependent O60264 188380 325680 193290 0 0 0 regulator of chromatin subfamily A member 5 HNRPR_HUMAN Heterogeneous nuclear O43390 169800 350720 408300 0 0 0 ribonucleoprotein R

P35249 RFC4_HUMAN Replication factor C subunit 165780 1014700 320010 0 0 0 4

Q14244 MAP7_HUMAN Ensconsin 163840 839550 328670 0 0 0 TRA2B_HUMAN Transformer-2 protein P62995 161560 310360 0 0 0 0 homolog beta PCH2_HUMAN Pachytene checkpoint Q15645 160470 515240 0 0 0 0 protein 2 homolog RRP1_HUMAN Ribosomal RNA processing P56182 159190 115810 145080 0 0 0 protein 1 homolog A

P18124 RL7_HUMAN 60S ribosomal protein L7 157330 330090 302730 0 0 0

RFC2_HUMAN Replication factor C subunit P35250 157000 201230 340140 0 0 0 2 GLYM_HUMAN Serine P34897 152110 124930 300600 0 0 0 hydroxymethyltransferase, mitochondrial

DDX18_HUMAN ATP-dependent RNA Q9NVP1 146560 419890 273150 0 0 0 helicase DDX18 WDR46_HUMAN WD repeat-containing O15213 145040 72416 0 0 0 0 protein 46 PYC_HUMAN Pyruvate carboxylase, P11498 143830 277740 178210 0 0 0 mitochondrial Q9H307 PININ_HUMAN Pinin 139290 262970 0 0 0 0 KHDR1_HUMAN KH domain-containing, Q07666 RNA-binding, signal 139080 0 223100 0 0 0 transduction-associated protein 1 STML2_HUMAN Stomatin-like protein 2, Q9UJZ1 138130 178460 106580 0 0 0 mitochondrial

P23396 RS3_HUMAN 40S ribosomal protein S3 136980 396430 198570 0 0 0

CISY_HUMAN Citrate synthase, O75390 136520 614880 236830 0 0 0 mitochondrial

P18887 XRCC1_HUMAN DNA repair protein XRCC1 130790 220870 147310 0 0 0

LAP2A_HUMAN Lamina-associated P42166 130250 476500 158050 0 0 0 polypeptide 2, isoform alpha

NU153_HUMAN Nuclear pore complex P49790 130100 150480 52522 0 0 0 protein Nup153 CDC5L_HUMAN Cell division cycle 5-like Q99459 124350 86884 0 0 0 0 protein SAHH2_HUMAN S-adenosylhomocysteine O43865 123420 215790 136650 0 0 0 hydrolase-like protein 1 ADAS_HUMAN O00116 Alkyldihydroxyacetonephosphate synthase, 122230 80850 68424 0 0 0 peroxisomal MCM5_HUMAN DNA replication licensing P33992 117410 149640 67449 0 0 0 factor MCM5 RRP1B_HUMAN Ribosomal RNA processing Q14684 116310 290610 0 0 0 0 protein 1 homolog B O43707 ACTN4_HUMAN Alpha-actinin-4 114120 215530 93161 0 0 0 EIF3F_HUMAN Eukaryotic translation O00303 112890 150140 103590 0 0 0 initiation factor 3 subunit F CAPZB_HUMAN F-actin-capping protein P47756 112390 1348100 339650 0 0 0 subunit beta

RPN1_HUMAN P04843 Dolichyl-diphosphooligosaccharide--protein 111220 139560 138570 0 0 0 glycosyltransferase subunit 1 Q16643 DREB_HUMAN Drebrin 110360 225880 170400 0 0 0 P49916 DNLI3_HUMAN DNA ligase 3 103240 203300 123560 0 0 0 AL3A2_HUMAN Fatty aldehyde P51648 102010 173020 0 0 0 0 dehydrogenase DSRAD_HUMAN Double-stranded P55265 101200 123010 37017 0 0 0 RNA-specific adenosine deaminase PABP1_HUMAN Polyadenylate-binding P11940 99111 267240 156480 0 0 0 protein 1

GNL3_HUMAN Guanine nucleotide-binding Q9BVP2 98873 503800 365000 0 0 0 protein-like 3 PWP2_HUMAN Periodic tryptophan protein Q15269 98123 70076 0 0 0 0 2 homolog DDX47_HUMAN Probable ATP-dependent Q9H0S4 97389 163290 132120 0 0 0 RNA helicase DDX47 PO210_HUMAN Nuclear pore membrane Q8TEM1 95299 271420 69850 0 0 0 glycoprotein 210

Q8TDM6 DLG5_HUMAN Disks large homolog 5 94470 130610 46036 0 0 0

PTBP1_HUMAN Polypyrimidine P26599 93769 112360 90306 0 0 0 tract-binding protein 1 CENPB_HUMAN Major centromere P07199 92902 61710 0 0 0 0 autoantigen B GANAB_HUMAN Neutral alpha-glucosidase Q14697 90901 316260 0 0 0 0 AB

Q71RC2 LARP4_HUMAN La-related protein 4 87611 136530 121450 0 0 0

IQGA1_HUMAN Ras GTPase-activating-like P46940 86227 318190 108130 0 0 0 protein IQGAP1

TR150_HUMAN Thyroid hormone Q9Y2W1 85653 284680 101700 0 0 0 receptor-associated protein 3 HIC2_HUMAN Hypermethylated in cancer 2 Q96JB3 83346 146180 0 0 0 0 protein PLOD3_HUMAN Multifunctional O60568 procollagen lysine hydroxylase and 83025 115080 70712 0 0 0 glycosyltransferase LH3 MYPT1_HUMAN Protein phosphatase 1 O14974 82921 287640 96846 0 0 0 regulatory subunit 12A

Q9H0D6 XRN2_HUMAN 5-3 2 81020 326420 152390 0 0 0

METK2_HUMAN S-adenosylmethionine P31153 80734 219310 114850 0 0 0 synthase isoform type-2 MCM3_HUMAN DNA replication licensing P25205 80495 221350 0 0 0 0 factor MCM3 RFC1_HUMAN Replication factor C subunit P35251 78829 64915 115290 0 0 0 1 RIR1_HUMAN Ribonucleoside-diphosphate P23921 75753 230970 99336 0 0 0 reductase large subunit

HS90A_HUMAN Heat shock protein HSP P07900 72216 86787 0 0 0 0 90-alpha SND1_HUMAN Staphylococcal nuclease Q7KZF4 71003 142990 67186 0 0 0 domain-containing protein 1

Q13435 SF3B2_HUMAN Splicing factor 3B subunit 2 68809 181070 36259 0 0 0

Q00610 CLH1_HUMAN Clathrin heavy chain 1 64733 78314 52786 0 0 0

NOG1_HUMAN Nucleolar GTP-binding Q9BZE4 64486 650720 513370 0 0 0 protein 1 TBL3_HUMAN Transducin beta-like protein Q12788 64293 52795 28418 0 0 0 3 P01024 CO3_HUMAN Complement C3 63547 50313 0 0 0 0 BAZ1B_HUMAN Tyrosine-protein kinase Q9UIG0 63203 135840 69042 0 0 0 BAZ1B WDR36_HUMAN WD repeat-containing Q8NI36 61670 74340 23932 0 0 0 protein 36 FXR2_HUMAN Fragile X mental retardation P51116 61085 114380 221660 0 0 0 syndrome-related protein 2

U5S1_HUMAN 116 kDa U5 small nuclear Q15029 59485 158450 48841 0 0 0 ribonucleoprotein component Q99590 SCAFB_HUMAN Protein SCAF11 59241 34216 0 0 0 0 DDX27_HUMAN Probable ATP-dependent Q96GQ7 58516 195860 127700 0 0 0 RNA helicase DDX27 SYMC_HUMAN Methionine--tRNA ligase, P56192 58047 129100 110550 0 0 0 cytoplasmic

Q9NW13 RBM28_HUMAN RNA-binding protein 28 54405 271460 78016 0 0 0

TCPD_HUMAN T-complex protein 1 subunit P50991 54183 120290 65922 0 0 0 delta SP16H_HUMAN FACT complex subunit Q9Y5B9 53644 227030 69410 0 0 0 SPT16 Q8WYP5 ELYS_HUMAN Protein ELYS 52507 192690 50772 0 0 0

Q14966 ZN638_HUMAN Zinc finger protein 638 49804 81488 53384 0 0 0 PFKAL_HUMAN ATP-dependent P17858 48961 320260 0 0 0 0 6-, liver type Q6ZRV2 FA83H_HUMAN Protein FAM83H 45629 159800 55504 0 0 0 P5CS_HUMAN P54886 41280 29062 40468 0 0 0 Delta-1-pyrroline-5-carboxylate synthase DDX56_HUMAN Probable ATP-dependent Q9NY93 40986 106670 0 0 0 0 RNA helicase DDX56

PCM1_HUMAN Pericentriolar material 1 Q15154 30847 34203 0 0 0 0 protein TCPH_HUMAN T-complex protein 1 subunit Q99832 30527 23387 86933 0 0 0 eta

Q14690 RRP5_HUMAN Protein RRP5 homolog 29058 161880 0 0 0 0

Q13085 ACACA_HUMAN Acetyl-CoA carboxylase 1 25670 10796 9743 0 0 0

Q02880 TOP2B_HUMAN DNA topoisomerase 2-beta 24144 227530 92293 0 0 0

ZCCHV_HUMAN Zinc finger CCCH-type Q7Z2W4 24098 0 45848 0 0 0 antiviral protein 1

P48681 NEST_HUMAN Nestin 23513 57119 0 0 0 0 O75369 FLNB_HUMAN Filamin-B 23393 41285 16552 0 0 0 DDX31_HUMAN Probable ATP-dependent Q9H8H2 21215 0 22707 0 0 0 RNA helicase DDX31 P58107 EPIPL_HUMAN Epiplakin 20125 96022 42310 0 0 0 DHX30_HUMAN ATP-dependent RNA Q7L2E3 19607 108830 20453 0 0 0 helicase DHX30 YLPM1_HUMAN YLP motif-containing P49750 18460 13947 0 0 0 0 protein 1

Q8WWI1 LMO7_HUMAN LIM domain only protein 7 18380 89939 62435 0 0 0

DYHC1_HUMAN Cytoplasmic dynein 1 Q14204 7867.2 21154 0 0 0 0 heavy chain 1

ABLM1_HUMAN Actin-binding LIM protein O14639 0 87604 61315 0 0 0 1 RRP8_HUMAN Ribosomal RNA-processing O43159 0 89673 87899 0 0 0 protein 8 RL1D1_HUMAN Ribosomal L1 O76021 0 499410 74041 0 0 0 domain-containing protein 1 OAT_HUMAN Ornithine aminotransferase, P04181 0 222450 172740 0 0 0 mitochondrial

P04792 HSPB1_HUMAN Heat shock protein beta-1 0 265010 121090 339220 0 0

ATPB_HUMAN ATP synthase subunit beta, P06576 0 202150 129200 248930 0 0 mitochondrial ODPA_HUMAN Pyruvate dehydrogenase E1 P08559 component subunit alpha, somatic form, 0 107760 143110 0 0 0 mitochondrial HSP76_HUMAN Heat shock 70 kDa protein P17066 0 364120 296650 0 0 0 6 UBA1_HUMAN Ubiquitin-like P22314 0 71597 63373 0 0 0 modifier-activating enzyme 1

P27635 RL10_HUMAN 60S ribosomal protein L10 0 1844800 1239400 0 0 0

PRS7_HUMAN 26S proteasome regulatory P35998 0 85337 29544 0 0 0 subunit 7 RFC5_HUMAN Replication factor C subunit P40937 0 320380 90758 0 0 0 5 VDAC2_HUMAN Voltage-dependent P45880 0 765380 580130 0 0 0 anion-selective channel protein 2

P47914 RL29_HUMAN 60S ribosomal protein L29 0 1277200 845290 0 0 0

TCPQ_HUMAN T-complex protein 1 subunit P50990 0 213200 30967 0 0 0 theta

P53396 ACLY_HUMAN ATP-citrate synthase 0 41152 53905 0 0 0

P61353 RL27_HUMAN 60S ribosomal protein L27 0 866760 339230 0 0 0

PRS4_HUMAN 26S proteasome regulatory P62191 0 125130 102430 0 0 0 subunit 4

P62241 RS8_HUMAN 40S ribosomal protein S8 0 1448200 467970 0 0 0

P62424 RL7A_HUMAN 60S ribosomal protein L7a 0 2727300 1143600 0 0 0

P62906 RL10A_HUMAN 60S ribosomal protein L10a 0 4657200 1836200 0 0 0

GTF2I_HUMAN General transcription factor P78347 0 151350 75647 0 0 0 II-I PRKDC_HUMAN DNA-dependent protein P78527 0 27283 20556 0 0 0 kinase catalytic subunit M2OM_HUMAN Mitochondrial Q02978 0 574920 485760 0 0 0 2-oxoglutarate/malate carrier protein GFPT1_HUMAN Q06210 Glutamine--fructose-6-phosphate 0 25089 23821 0 0 0 aminotransferase [isomerizing] 1

TADBP_HUMAN TAR DNA-binding protein Q13148 0 541700 276590 0 0 0 43 PSMD2_HUMAN 26S proteasome Q13200 0 86475 59336 0 0 0 non-ATPase regulatory subunit 2 SRSF6_HUMAN Serine/arginine-rich Q13247 0 248690 100050 0 0 0 splicing factor 6

Q13547 HDAC1_HUMAN Histone deacetylase 1 0 224350 166730 0 0 0

Q14498 RBM39_HUMAN RNA-binding protein 39 0 65048 62714 59025 0 0

Q15365 PCBP1_HUMAN Poly(rC)-binding protein 1 0 796460 522630 0 0 0

Q15393 SF3B3_HUMAN Splicing factor 3B subunit 3 0 128520 37819 0 0 0 SAFB1_HUMAN Scaffold attachment factor Q15424 0 182050 0 0 0 0 B1 Q15517 CDSN_HUMAN Corneodesmosin 0 0 0 725290 0 0 GLYR1_HUMAN Putative Q49A26 0 50906 0 0 0 0 GLYR1

Q562R1 ACTBL_HUMAN Beta-actin-like protein 2 0 0 69910000 0 0 0

ZN326_HUMAN DBIRD complex subunit Q5BKZ1 0 132860 0 0 0 0 ZNF326 CI114_HUMAN Putative methyltransferase Q5T280 0 107210 0 0 0 0 C9orf114

LRIF1_HUMAN Ligand-dependent nuclear Q5T3J3 0 380350 0 0 0 0 receptor-interacting factor 1 RGPA1_HUMAN Ral GTPase-activating Q6GYQ0 0 0 66439 0 0 0 protein subunit alpha-1 ATAD2_HUMAN ATPase family AAA Q6PL18 0 84876 30809 0 0 0 domain-containing protein 2 Q6UWP8 SBSN_HUMAN Suprabasin 0 0 0 1609800 0 0 MPRIP_HUMAN Myosin phosphatase Q6WCQ1 0 228010 47116 0 0 0 Rho-interacting protein

Q7Z7K6 CENPV_HUMAN Centromere protein V 0 471380 505360 0 0 0

PABP2_HUMAN Polyadenylate-binding Q86U42 0 353980 110180 0 0 0 protein 2

Q86V48 LUZP1_HUMAN Leucine zipper protein 1 0 0 73244 0 0 0

ZSWM9_HUMAN Uncharacterized protein Q86XI8 0 0 0 198290 0 0 ZSWIM9 PELP1_HUMAN Proline-, glutamic acid- and Q8IZL8 0 130090 0 0 0 0 leucine-rich protein 1

AFAP1_HUMAN Actin filament-associated Q8N556 0 0 209440 0 0 0 protein 1 ICA1L_HUMAN Islet cell autoantigen 1-like Q8NDH6 0 0 0 0 0 0 protein DDX54_HUMAN ATP-dependent RNA Q8TDD1 0 186170 102270 0 0 0 helicase DDX54 GCN1_HUMAN eIF-2-alpha kinase activator Q92616 0 67879 11830 0 0 0 GCN1 ROAA_HUMAN Heterogeneous nuclear Q99729 0 441790 316100 0 0 0 ribonucleoprotein A/B RPF2_HUMAN Ribosome production factor Q9H7B2 0 610120 237680 0 0 0 2 homolog

SLTM_HUMAN SAFB-like transcription Q9NWH9 0 410880 124210 0 0 0 modulator

Q9UKM9 RALY_HUMAN RNA-binding protein Raly 0 134690 95658 0 0 0 Q9ULW0 TPX2_HUMAN Targeting protein for Xklp2 0 61976 64138 0 0 0

DDX52_HUMAN Probable ATP-dependent Q9Y2R4 0 86060 163340 0 0 0 RNA helicase DDX52

Q9Y2X3 NOP58_HUMAN Nucleolar protein 58 0 1709200 68555 0 0 0

TF3C3_HUMAN General transcription factor Q9Y5Q9 0 48118 27435 0 0 0 3C polypeptide 3